Gault later told Desmond and Sayid to leave the freighter, but Desmond insisted on staying on the freighter. Sayid then was given the Zodiac raft by Gault so he could travel back to the island to start ferrying survivors back to the Kahana. Gault told Sayid to make sure he navigated the raft on a bearing of 305. ("Cabin Fever") When Sayid arrived on the Island Faraday took over and took six survivors, including Aaron, Sun, and Jin to the Kahana. ("There's No Place Like Home, Part 1") After successfully finishing the first trip Daniel, knowing about secondary protocol, asked both Charlotte and Miles to be with him on the second trip, which he may have known would be the last one. Both of them refused though, choosing to stay on the Island, so Daniel took another five survivors of Flight 815. The raft was in the ocean when the sky lit up, followed by the disappearance of the Island. The Zodiac raft with everyone on it was in the Island's radius, and was moved with the Island. Daniel returned the Zodiac to the beach. ("The Lie") Several flashes later, Sawyer and his group found the Zodiac raft missing. ("The Little Prince")

The survivors and freighties along with Juliet prepare the raft for its first trip to the Kahana.

Trivia

The passengers of the second trip return to the Island after it moves. ("Because You Left")

In the Season 4 finale, the raft left the beach with Daniel, Craig, Steve Jenkins, and three unnamed passengers (Lisa R., Steve Tanizaki and Unknown #1 according to Background cast/middle section survivors). However in the premiere of Season 5, the raft returned with Daniel, Craig, two unnamed passengers (Lisa R. and Unknown #1) and then Neil, who was not seen aboard the raft in Season 4. In addition to Neil suddenly appearing on the raft, Steve Jenkins and a background survivor, played by Steve Tanizaki, were not on the raft returning to the beach in Season 5.